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Odaiba seaside park is one of the most popular waterfronts in Tokyo Bay, but is easily affected by wet weather pollutant loads through combined sewer overflows (CSOs). The monitoring data of Escherichia coli clearly showed high faecal contamination after a rainfall event on 9–11 November 2007. We estimated the amounts of discharge volume and E. coli pollutant loads of urban rivers receiving CSO from rainfall chambers as well as pumping stations and primary effluent discharge. The result suggested that Sumida River and Meguro River were more influential to the Odaiba coastal area than other sources including the nearest wastewater treatment plant. Subsequently, we simulated the dynamic behaviour of E. coli by a three-dimensional (3D) hydro-dynamic and water quality model. The model simulation reproduced that E. coli concentration after the rainfall event increased rapidly at first and later gradually decreased. The simulations with and without inflow pollutant loads from urban rivers suggested that the E. coli concentration can be influenced by the Meguro River just after the rainfall event and Sumida River about 1 week later. From the spatial and temporal distribution of surface E. coli concentration, after at least 6 days from the rainfall event, high faecal contamination spread to the whole of the coastal area.